Dear Smith, It is not possible to give the whole exact commands because it depends on which atoms and which chains you want to use for the calculation. However, to get you started, the commands to use would be (A) “measure buriedArea” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea> (B) “define plane” (once for each domain) and then “angle” on the resulting two planes <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#plane> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> You’d have to specify the relevant sets of atoms as well as any other command options you might want to use. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 4, 2016, at 2:23 AM, Smith Liu <smith_liu123@163.com> wrote:

Dear All,

Will you please tell me the command to calculate the contact surface area between 2 sub-units in the protein complex? Will you please also tell me the command to calculate the angle in degree between 2 domains in a subunit?

Smith